Stay through the night
by hookspirateswan
Summary: Prompt found on Irishswanff's tumblr: Emma and Killian are sleeping together, Emma only realises she's pregnant in the middle of a miscarriage, she doesn't tell anyone even though everyone in town knows about her and Killian anyway. Dr whale see's Emma in hospital and calls Killian.
1. Chapter 1

**A/N: So this is a prompt i found on IrishSwanff's tumblr, I made it a modern AU since that was easier to write. I don't know how many parts this will have i'm thinking maybe 2 or 3 who knows so anyway enjoy part 1 and please review xx**

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Emma's eyes snapped open and immediately groaned inwards at the intrusive bleeping of an alarm clock that didn't belong to her, whilst the alarm was set for her it wasn't her alarm clock she just used her phone and had a less obnoxious sound to wake her up with but Killian had to be an actual adult and have a separate device just for telling you when to wake up despite technology allowing you to do that and multiple other things from one device secretly she found it cute and endearing that he had to have an alarm clock because that supposedly what an adult was supposed to own not that she would ever say that out loud,to him of course.

Just as Emma was about to get up an arm shot out from next to her to turn the alarm off before coming to rest on her stomach and pull her closer to the center of the bed closer to Killian's chest, she hummed as his hand found its way under her well his shirt.

"I have to get up" she groaned as his hand moved further up her stomach.

"Mm s'early love" was he replied before burying his face into her neck and mumbling "Go back to sleep love" and whilst he wasn't wrong as it was early it was 5:30 that was the point she was supposed to leave before anyone could see that she spent the night at Killian's just as he was supposed to leave her place early when he spent the night there. To which she told him as much only to have him grumble something incoherent and tightened his hold on her, no one was supposed to know that Storybrookes two deputies were sleeping together and secretly in a relationship but today he was making it difficult for her, he never usually grumbled this much when she had to leave to go home because he would see her in three hours when he would be waiting outside the station for her with her morning coffee from Granny's, so why is he making it so difficult for her today she wondered.

She rolled over to face him, he had his eyes closed clearly trying to chase down sleep again for what little time he had before he would have to get up his hair was disheveled in a way that in the early morning light made him look younger, he looked peaceful she thought there was no trace of any of the pain he'd faced in his life, she gently moved to push the hair back from his face that had fallen forward in front of his eyes.

"Killian" she whispered trying to carefully rouse him again"Killian I need to go I'll see you at the station" he didn't move assuming he had fallen back asleep she pressed a light kiss onto his forehead and got up and began to dress. Once she was dressed she began to move towards the bedroom door to leave the apartment when she heard the bed sheets move and Killian spoke up

"why?" he asked in an irritated tone, was he angry with her she wondered, if so why? This is what they always did, this was what they agree'd to 9 months ago when they they first started seeing each other.

"why what?" she huffed and turned around to face him he was sitting up with the sheet pooling low at his hips, it has to illegal for someone to look that good at half five in the morning she thought.

"why the sneaking around, why the having to leave at half five in the bloody morning when we could get up at a normal time and just go to work together like normal people would, Emma its been nine months! why the secrecy still?" he tilted his head with the last question in exasperation.

"why is this suddenly an issue for you now?" her voice rising as the irrational fears and thoughts ran through her head, why wasn't this enough for him? why did he need people to know? does this mean he's going to just leave like everyone else that was close to her? is she too difficult for him and he's giving up on her, despite what he always tells her that he's in this for the long haul?

"BECAUSE MAYBE I WANT TO BE ABLE TO TAKE THE WOMEN I LOVE OUT AND NOT HAVE TO WORRY ABOUT PEOPLE SEEING!" He shouted back, her mind was racing through so much that she almost missed what he said entirely except for the one word that broke through her thoughts like a bullet through a thin pane of glass and bounced around her mind as loud as the alarm clock did earlier.

Love. He couldn't mean it, surely not it had only been nine months and even then she wasn't a person who could be loved, Neal made sure of that and just when she thought otherwise Graham had shattered that thought and then later Walsh had cemented the deep foundation of the walls around her heart that Neal had forced her to put up all those years ago. So yeah she was pretty sure Killian couldn't possibly mean it when he said that and she was pretty sure he would probably be taking it back any second now and with the panic rising inside her she didn't want to wait around to find out, so Emma Swan did what she did best and ran leaving a hurt looking Killian in her wake.

He sat and watched as what he had just said registered in her head more specific as a certain word he hadn't quite meant to say registered. Love. out of the things to say to her why did he have to say bloody love, he meant it of course in fact he'd been in love with her for a long time a lot longer than the nine months they had actually been together, he's pretty sure he's been in love with Emma Swan since he came to Storybrooke 2 and a half years ago after his friends Victor and Robin told him he should try it and get out of the city and place that was causing him more pain than anything they practically dragged him here and pushed him into the sheriffs station that day to apply for the deputy position.

Walking into what he supposed was the main room and bullpen of the station he was met by no one until he heard what has now became one of his favourite sounds in the world, he spun on his heels and it was then when he saw her for the first time sitting on the corner of her adopted brother David Nolan's desk, who happened to be the sheriff and still is, she was laughing a real laugh with her head thrown back and everything her light blonde curls tumbling over her shoulder and down her back like a goddess and her emerald eyes shining like the precious gem they resembled when she fully turned to look at him he was a goner she introduced herself with a shy smile before biting her lip when their eyes met.

He knew as soon as he said the word love it was a . he thought to himself as if becoming more disgusted with the word by the second he knew Emma wasn't ready to hear how deep his feeling for her ran mainly because she doesn't think she deserves to be loved which he can understand but cant possibly see ow anyone could meet her and not fall for her its utterly impossible, but the fact of the matter now is he did say it and as he predicted she ran literally and figuratively whilst she may of physically ran to her apartment he knows she emotionally ran behind her skyscraper walls that he was attempting to scale and was possibly more than halfway up and now because of one word, love, she's pushed them up higher and he fell back down to the bottom looking up to start again. Fuck he cursed to no one but himself he'd fucked up everything they had built with one fucking word. Love.

Killian groaned and flopped backwards on to the bed again and closed his eyes in frustration jut as a loud obnoxious beeping started up again. it was his alarm clock the timer for snooze and gone off it had only been 15 minutes since they woke up and in that 15 minutes everything had changed gotten messy, blindly Killian reached for the button on the clock, unable to find the button he grabbed the alarm and threw it against the wall causing it to smash. He groaned to himself again and put wiped his hand across his face trying to figure out how to fix what he'd broke.


	2. Chapter 2

I'm so so so sorry this took so long to update life just kept getting in the way and then Uni but I hope this makes up for it? Also this is unedited so sorry for any mistakes xx

Emma's feet pounded the stairs as she ran up the stairs to her apartment and slammed the door behind her before leaning on it and breathing heavily, she knew she shouldn't of ran out on Killian like that, she knew he didn't deserve it, but he said things that made her mind run a hundred miles an hour.

Now though she was worried she had royally fucked everything up, that he'd back what he she want him to take back what he said? Did he actually mean it when he said he loved her the thought made her smile but she shook her head to rid herself of the though she didn't really want to dwell on it if next time they saw each other he was going to take it back. Before she could begin to even think about it she found herself sprinting to the bathroom to empty the non existent content of her stomach into the toilet. She gently rested her head against the cool porcelain and thought about the fact the that this was the second morning in a row that this had happened at first she brushed it off as she didn't feel sick, she thought of another possibility but pushed it out her mind quickly because it was impossible she couldn't be once again she rid herself of the thought and summed it up as having ate something bad. Emma picked herself up off the bathroom floor and began to get ready for the day.

Emma pulled her bug into her usual parking space at the station, just as she was about to get out something caught her eye in the side mirror or rather nothing caught her eye, Killian wasn't standing waiting for her with two to go cups from Granny's like he usually was she looked around as she stepped out the car only to be hit with the realisation that Killian wasn't waiting her. Suddenly hit with a feeling of disappointment she quickly brushed it off as she headed into the station and told herself that it was cold he was probably just waiting inside despite the man being a walking radiator and never needing wrap up unlike emma who almost always had to be wearing her beanie and gloves when going outside but hey it was winter and they were in Maine who could blame her.

As she walked down the hall into the main room of the station she was hit with another wave of disappointment and sadness? no why would she be sad that Killian wasn't waiting outside for her or inside as she only noticed David in his office doing paper work and the empty desks that belonged to herself and Killian.

"He's out on morning patrol" Emma spun around to face David who had stopped doing his work and evidently noticed her looking for Killian, Emma opened her mouth to ask her brother what he meant but he cut in again before she got the chance "Offered to switch with me if I would take his tonight. Are you guys okay?" Emma was stunned that he would ask if they were okay its not like David knew they were together she suspected some of the other townspeople might of guessed about the two deputies but Emma knew David was clueless to the fact that his sister and one of his closest friends were sleeping together "yeah every things fine why would you ask that?"she tried to sound as disinterested and non committed as she could as she turned away and sat down at her desk, she internally groaned as she heard David getting up from his chair.

David who was obviously not going to let the conversation go " Because he also offered to go Regina's office for me this morning for the monthly report." he was standing at the doorway giving Emma a pointed look to this though Emma just shrugged and picked up a file from the pile on the desk and flipped it open "Killian, who we all know can't stand to be around Regina for more than 10 minutes offered to go to an hour long meeting with her."

Emma knew fine well the issues Killian had with Regina and the ones Regina had with him which meant Killian willingly going to the monthly meeting with her only confirmed her suspicions that she had in fact fucked everything up and now Killian was avoiding her. Which she had to admit hurt and made her angry if anything she should want to avoid him and run after this morning but some reason around Killian Emma found herself not wanting to run and that scared her more than anything. before she got to deep into thought she realised David was still standing At the door to his office probably waiting for her to reply.

"I don't know David." she managed to huff out without looking up from the file she wasn't actually reading and he probably knew it. David sighed but let it go when the phone started to ring. Once David had shut the door to his office to answer the phone Emma looked up from the file before leaning back on her chair, she pulled out her phone only to see no missed calls or texts from Killian she swiped her finger across the screen to unlock it and hovered her finger above Killian's name on her contact list as she hesitated wondering if she should call him or not she was about to hit the call button when her stomach suddenly lurched forwards and for the second time this morning Emma found herself running towards the toilet.

As she sat on the on the cold toilet floor of the station he leaned back against the wall and closed her eyes, after less than a minute the phone in her hand started to buzz he opened her eyes and looked down at the screen to see who was calling. She took a deep breathe in when she saw who was calling.

Killian.

Killian knew he shouldn't avoid Emma and that it was he childish thing to do but he also told himself that he wasn't really avoiding her it was more he was giving her space until he knew how to fix things, he didn't want to take back what he said because it was true he loved her and wasn't going to deny it, he just didn't want to have to hide the fact that he loved Emma Swan.

Just then a repetitive and down right annoying snapping noise brought him out of his thoughts, it was then that he realised he was still sitting in Regina's office for the monthly report that he regrettably told David he go to in order to not have to face Emma. The fact that he was willingly sitting in Regina's office at all was a testament to how big a coward he was being with this whole situation between Emma and himself and he knew it. He also knew if he kept zoning out like this then Regina was going to be worse than her usual self, another round of snapping fingers brought him back to find Regina sitting across from him looking rather unimpressed, he looked at her expectedly as if he'd done nothing wrong and waited for her to speak.

Regina huffed and calmly set her hands back on the desk before sitting back up straight in her self in her usual regal demeanour

"Deputy Jones if you were just going to sit there and blatantly ignore everything I had to say I'm not sure why you offered to come instead of the Sheriff." Regina raised an eyebrow waiting for a response.

"Apologise Mayor Mills" he responded pouring all his sarcasm into it "what else do you have to add? As far as I'm aware you usually just say the same thing every month to David it's not like much ever changes round here so I'm sure he'll understand if I just tell him that you said the usual." Regina looked taken back by Killian's blatant lack of respect though not overly surprised. "Besides", he added "I have bigger issues than sitting here listening to you talk about arrest numbers when you know fine well the only person we really ever arrest is Leroy or is there a criminal gang going round Storybrooke that only you know of?"

The fact that Regina was silent was the biggest indication that he probably shouldn't of snapped but his bigger concern was the almost sympathetic look on her face that he couldn't quite figure out why it was there. Regina closed the file she had opened and held it out towards him,

"What ever is going on between you and Miss Swan will surely work itself out, you made it this far didn't you?" Regina stood with the file in her hand as Killian slowly took it from her as he made a half hearted attempt to shut down what she was insinuating

"I don't know what your talkin-"

"We aren't all as blind and clueless as the two of you would like to believe Jones, now go talk to her so you don't have to come to another meeting here for my sake and your own" Killian's mouth twitched up at one side and gave her a small nod before leaving her office wondering how the hell Regina knew about the two of them.

As he walked out of the Town Hall Killian knew he had to talk to Emma whether she really wanted to or not. If Regina knew about them then other people had to know as well right? And if people already knew then it wasn't really a secret anymore so they could just stop sneaking around. Right? Killian fished his phone out of his pocket as he got into the car and hoped Emma would answer.

Time almost slowed down for Killian after each ring and Emma wouldn't pick up, he was about to give up when he heard her unusually quiet hello

"Emma?"

I don't know if people are still reading this given it took so long to update but if you are thank you and I promise I won't take as long to update next time...probably xx


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